Nanofiltration membrane separation is an energy-saving technology that was used in this study to concentrate extracellular lipase and increase its total activity for biodiesel production. Lipase was produced by recombinant Aspergillus oryzae expressing Fusarium heterosporum lipase (FHL). A sulfonated polyethersulfone nanofiltration membrane, NTR-7410, with a molecular weight cut-off of 3 kDa was used for the separation, because recombinant lipase has a molecular weight of approximately 20 kDa, which differs from commercial lipase at around 30 kDa for CalleraTM Trans L (CalT). After concentration via nanofiltration, recombinant lipase achieved a 96.8% yield of fatty acid methyl ester (FAME) from unrefined palm oil, compared to 50.2% for CalT in 24 h. Meanwhile, the initial lipase activity (32.6 U/mL) of recombinant lipase was similar to that of CalT. The composition of FAME produced from recombinant concentrated lipase, i.e., C14:1, C16:0, C18:0, C18:1 cis, and C18:2 cis were 0.79%, 34.46%, 5.41%, 45.90%, and 12.46%, respectively, after transesterification. This FAME composition, even after being subjected to nanofiltration, was not significantly different from that produced from CalT. This study reveals the applicability of a simple and scalable nanofiltration membrane technology that can enhance enzymatic biodiesel production.